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OpenMS
2.5.0
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Go to the documentation of this file.
101 virtual void run(
const std::vector<Peak2D> & map_model,
const std::vector<Peak2D> & map_scene,
TransformationDescription & transformation);
112 return "poseclustering_affine";
void addMSLevel(int level)
adds a desired MS level for peaks to load
Management and storage of parameters / INI files.
Definition: Param.h:73
Size findNearest(CoordinateType mz) const
Binary search for the peak nearest to a specific m/z.
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Helper class for looking up spectra based on different attributes.
Definition: SpectrumLookup.h:67
Implementation of the Ascore For a given peptide sequence and its MS/MS spectrum it identifies the mo...
Definition: AScore.h:70
MSSpectrum & getSpectrum(Size id)
returns a single spectrum
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:121
static const String getProductName()
Returns the name of this module.
Definition: PoseClusteringAffineSuperimposer.h:110
bool metaValueExists(const String &name) const
Returns whether an entry with the given name exists.
Size findByRT(double rt) const
Look up spectrum by retention time (RT).
const AASequence & getSequence() const
returns the peptide sequence without trailing or following spaces
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:61
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
String toString() const
returns the peptide as string with modifications embedded in brackets
void clearMSLevels()
clears the MS levels
const double C13C12_MASSDIFF_U
A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transf...
Definition: PoseClusteringAffineSuperimposer.h:66
Base class for TOPP applications.
Definition: TOPPBase.h:144
PeptideHit compute(const PeptideHit &hit, PeakSpectrum &real_spectrum)
Computes the AScore and returns all computed phospho-sites. The saved sequences contain only phospho ...
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
void sortByPosition()
Lexicographically sorts the peaks by their position.
CoordinateType getMZ() const
Non-mutable access to m/z.
Definition: Peak1D.h:115
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
The base class of all superimposer algorithms.
Definition: BaseSuperimposer.h:56
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
Logger::LogStream OpenMS_Log_debug
Global static instance of a LogStream to capture messages classified as debug output....
const std::vector< MSSpectrum > & getSpectra() const
returns the spectrum list
A container for consensus elements.
Definition: ConsensusMap.h:79
const double PROTON_MASS_U
void setParameters(const Param ¶m)
Sets the parameters.
#define OPENMS_LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:470
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
bool update(const Param &p_outdated, const bool add_unknown=false)
Rescue parameter values from p_outdated to current param.
~PoseClusteringAffineSuperimposer() override
Destructor.
Definition: PoseClusteringAffineSuperimposer.h:76
bool hasSubstring(const String &string) const
true if String contains the string, false otherwise
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
const Param & getDefaults() const
Non-mutable access to the default parameters.
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
Used to load and store idXML files.
Definition: IdXMLFile.h:63
File adapter for MzML files.
Definition: MzMLFile.h:55
double getScore() const
returns the PSM score
void sortSpectra(bool sort_mz=true)
Sorts the data points by retention time.
A more convenient string class.
Definition: String.h:58
Representation of a peptide hit.
Definition: PeptideHit.h:54
void store(const String &filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
Stores the data in an idXML file.
static BaseSuperimposer * create()
Returns an instance of this class.
Definition: PoseClusteringAffineSuperimposer.h:104
void readSpectra(const SpectrumContainer &spectra, const String &scan_regexp=default_scan_regexp)
Read and index spectra for later look-up.
Definition: SpectrumLookup.h:103
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
void clear(bool clear_meta_data)
Clears all data and meta data.
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.